chr10-60803097-G-C

Variant names:

• chr10-60803097-G-C
• rs4145643

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.32 in 152,030 control chromosomes in the GnomAD database, including 7,955 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (7955 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48650 AN: 151912 Hom.: 7955 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.275

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.320 AC: 48664 AN: 152030 Hom.: 7955 Cov.: 32 AF XY: 0.323 AC XY: 23986 AN XY: 74298

African (AFR) AF: 0.287 AC: 11892 AN: 41454

American (AMR) AF: 0.265 AC: 4057 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 846 AN: 3468

East Asian (EAS) AF: 0.385 AC: 1983 AN: 5146

South Asian (SAS) AF: 0.266 AC: 1279 AN: 4814

European-Finnish (FIN) AF: 0.445 AC: 4702 AN: 10572

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23032 AN: 67974

Other (OTH) AF: 0.271 AC: 570 AN: 2104

Alfa AF: 0.216 Hom.: 538

Bravo AF: 0.304

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.7
DANN	Benign	0.59
PhyloP100		0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4145643; hg19: chr10-62562855;